Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

Odenkirk, Melanie T.; Zin, Phyo Phyo Kyaw; Ash, Jeremy R.; Reif, David M.; Fourches, Denis; Baker, Erin

doi:10.1039/d0an01638a

Cited by 20 publications

(20 citation statements)

References 57 publications

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“…and provides a heatmap of log2 fold change ratios relative to a control. 41 This enabled a spatial comparison of each spheroid layer to further visualize the lipidomic changes at both a subclass-wide and even on a lipid species-specific level. Using the 2D monolayer data for our baseline comparison, Figure 2 illustrates all the lipid abundance alterations in the three spheroid regions.…”

Section: Untargeted Lipidomics Profiling Of 2d Monolayer Cultures And...mentioning

confidence: 99%

Lipidomic comparison of 2D and 3D colon cancer cell culture models

Tobias

Hummon

2022

J Mass Spectrom

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Altered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids comprised of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in the tumor microenvironment that can be further studied to target pivotal lipid production pathways.

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Section: Untargeted Lipidomics Profiling Of 2d Monolayer Cultures And...mentioning

confidence: 99%

Lipidomic comparison of 2D and 3D colon cancer cell culture models

Tobias

Hummon

2022

J Mass Spectrom

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Section: Methodsmentioning

confidence: 99%

“…Lipidomic relationships were investigated using cheminformatics to interrogate structure-function associations across head groups and fatty acyl (FA) moieties [ 37 , 38 , 39 ]. Head group clustering was completed with the SCOPE toolbox [ 39 ]. Here, SMILES [ 40 ] obtained from LipidMaps [ 34 ] for each lipid identification were clustered by structural similarity using an ECFP_6 fingerprint [ 41 ], Tanimoto distance and complete linkage using the fingerprint and ggtree packages in R (Version 3.6.2, Vienna, Austria) [ 42 , 43 ].…”

Section: Methodsmentioning

confidence: 99%

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions

et al. 2020

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While a molecular assessment of the perturbations and injury arising from diseases is essential in their diagnosis and treatment, understanding changes due to preventative strategies is also imperative. Currently, complex diseases such as cardiovascular disease (CVD), the leading cause of death worldwide, suffer from a limited understanding of how the molecular mechanisms taking place following preventive measures (e.g., exercise) differ from changes occurring due to the injuries caused from the disease (e.g., myocardial infarction (MI)). Therefore, this manuscript assesses lipidomic changes before and one hour after exercise treadmill testing (ETT) and before and one hour after a planned myocardial infarction (PMI) in two separate patient cohorts. Strikingly, unique lipidomic perturbations were observed for these events, as could be expected from their vastly different stresses on the body. The lipidomic results were then combined with previously published metabolomic characterizations of the same patients. This integration provides complementary insights into the exercise and PMI events, thereby giving a more holistic understanding of the molecular changes associated with each.

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“…These approaches are employed to estimate adjustments in metabolites connected to lipid metabolism at variable exercise intensities and durations in body fluids such as blood and plasma [44]. A number of studies have proved that metabolomics and lipidomics may bring to light disorders in oxidative stress [45], abnormalities in energetic substrates used during physical exercise [46], and various metabolic phenotypes related to physiological parameters (i.e., VO 2max and lactate clearance capacity) [47].…”

Section: Lipidomic Analyses Of Biological Fluids Following Exercise: the Blood Rolementioning

confidence: 99%

The Importance of Lipidomic Approach for Mapping and Exploring the Molecular Networks Underlying Physical Exercise: A Systematic Review

Latino

Cataldi

Carvutto

et al. 2021

IJMS

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Maintaining appropriate levels of physical exercise is an optimal way for keeping a good state of health. At the same time, optimal exercise performance necessitates an integrated organ system response. In this respect, physical exercise has numerous repercussions on metabolism and function of different organs and tissues by enhancing whole-body metabolic homeostasis in response to different exercise-related adaptations. Specifically, both prolonged and intensive physical exercise produce vast changes in multiple and different lipid-related metabolites. Lipidomic technologies allow these changes and adaptations to be clarified, by using a biological system approach they provide scientific understanding of the effect of physical exercise on lipid trajectories. Therefore, this systematic review aims to indicate and clarify the identifying biology of the individual response to different exercise workloads, as well as provide direction for future studies focused on the body’s metabolome exercise-related adaptations. It was performed using five databases (Medline (PubMed), Google Scholar, Embase, Web of Science, and Cochrane Library). Two author teams reviewed 105 abstracts for inclusion and at the end of the screening process 50 full texts were analyzed. Lastly, 14 research articles specifically focusing on metabolic responses to exercise in healthy subjects were included. The Oxford quality scoring system scale was used as a quality measure of the reviews. Information was extracted using the participants, intervention, comparison, outcomes (PICOS) format. Despite that fact that it is well-known that lipids are involved in different sport-related changes, it is unclear what types of lipids are involved. Therefore, we analyzed the characteristic lipid species in blood and skeletal muscle, as well as their alterations in response to chronic and acute exercise. Lipidomics analyses of the studies examined revealed medium- and long-chain fatty acids, fatty acid oxidation products, and phospholipids qualitative changes. The main cumulative evidence indicates that both chronic and acute bouts of exercise determine significant changes in lipidomic profiles, but they manifested in very different ways depending on the type of tissue examined. Therefore, this systematic review may offer the possibility to fully understand the individual lipidomics exercise-related response and could be especially important to improve athletic performance and human health.

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Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

Abstract: Since its inception, the main goal of the lipidomics field has been to characterize lipid species and their respective biological roles. However, difficulties in both full speciation and biological interpretation...

Cited by 20 publications

References 57 publications

Lipidomic comparison of 2D and 3D colon cancer cell culture models

Lipidomic comparison of 2D and 3D colon cancer cell culture models

From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions

The Importance of Lipidomic Approach for Mapping and Exploring the Molecular Networks Underlying Physical Exercise: A Systematic Review

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